Maturation of canonical microRNA (miRNA) is initiated by DROSHA that cleaves the primary transcript (pri-miRNA). More than 1,800 miRNA loci are annotated in humans, but it remains largely unknown whether and at which sites pri-miRNAs are cleaved by DROSHA. Here, we performed in vitro processing on a full set of human pri-miRNAs (miRBase version 21) followed by sequencing. This comprehensive profiling enabled us to classify miRNAs on the basis of DROSHA dependence and map their cleavage sites with respective processing efficiency measures. Only 758 pri-miRNAs are confidently processed by DROSHA, while the majority may be non-canonical or false entries. Analyses of the DROSHA-dependent pri-miRNAs show key cis-elements for processing. We observe widespread alternative processing and unproductive cleavage events such as “nick” or “inverse” processing. SRSF3 is a broad-acting auxiliary factor modulating alternative processing and suppressing unproductive processing. The profiling data and methods developed in this study will allow systematic analyses of miRNA regulation. Display omitted •This study provides a quantitative map of 1,816 human pri-miRNA processing sites•Only 758 are confidently processed, while the majority are non-canonical or false entries•We uncover atypical events such as alternative, nick, and inverse processing•SRSF3 is a broad-acting cofactor modulating the majority of canonical pri-miRNAs More than 1,800 human miRNAs have been annotated, yet it remains unknown how many are authentic and canonical miRNAs. Kim et al. perform high-throughput in vitro processing to provide the first quantitative map of primary miRNA processing sites, which reveals their DROSHA dependence and enables miRNA classification.